This is an area I'm interested in but haven't quite got round to investigating properly. But can I suggest using the "toggle_fog" RomeShell command to remove the fog of war from your game. This should help you identify any bandits, ships, etc. affecting your trade.
Also, devastation seems to be a factor that only affects farming (and perhaps mining, harder to check) income. Although it doesn't seem to be subtracted from my income either, at least in any straightforward way.
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